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Detailed information for vg0322195173:

Variant ID: vg0322195173 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 22195173
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GCGCCCACGCCGTGTCGAGCTCCGCCCGCTCCGCCTGCAGGGCCTCCATCTGGGCACTTAACCCGTCCAGCACCGTGCTGTTCGCGGCGGCCAAGGCCTG[T/C]
AGGAAGGGCTCCACGCTCAGTGGGGCAGCGGAAGACGTGCCGGACTCGGGGGCGTCCCTCGAAGCTGGCTCGTCCCAAGTGTCGCCCGAGGGGTCGGGCC

Reverse complement sequence

GGCCCGACCCCTCGGGCGACACTTGGGACGAGCCAGCTTCGAGGGACGCCCCCGAGTCCGGCACGTCTTCCGCTGCCCCACTGAGCGTGGAGCCCTTCCT[A/G]
CAGGCCTTGGCCGCCGCGAACAGCACGGTGCTGGACGGGTTAAGTGCCCAGATGGAGGCCCTGCAGGCGGAGCGGGCGGAGCTCGACACGGCGTGGGCGC

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 6.00% 5.60% 20.40% 67.92% NA
All Indica  2759 0.20% 0.50% 25.12% 74.16% NA
All Japonica  1512 18.10% 16.30% 9.72% 55.89% NA
Aus  269 0.00% 0.00% 35.69% 64.31% NA
Indica I  595 0.00% 0.20% 17.14% 82.69% NA
Indica II  465 0.00% 0.60% 6.67% 92.69% NA
Indica III  913 0.20% 0.20% 44.69% 54.87% NA
Indica Intermediate  786 0.40% 1.10% 19.34% 79.13% NA
Temperate Japonica  767 4.60% 17.60% 11.86% 65.97% NA
Tropical Japonica  504 43.10% 13.10% 7.34% 36.51% NA
Japonica Intermediate  241 8.70% 19.10% 7.88% 64.32% NA
VI/Aromatic  96 0.00% 1.00% 15.62% 83.33% NA
Intermediate  90 7.80% 4.40% 14.44% 73.33% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0322195173 T -> C LOC_Os03g39930.1 5_prime_UTR_premature_start_codon_gain_variant ; LOW silent_mutation Average:14.149; most accessible tissue: Minghui63 panicle, score: 25.313 N N N N
vg0322195173 T -> C LOC_Os03g39930.1 5_prime_UTR_variant ; 52.0bp to feature; MODIFIER silent_mutation Average:14.149; most accessible tissue: Minghui63 panicle, score: 25.313 N N N N
vg0322195173 T -> C LOC_Os03g39920.1 downstream_gene_variant ; 2003.0bp to feature; MODIFIER silent_mutation Average:14.149; most accessible tissue: Minghui63 panicle, score: 25.313 N N N N
vg0322195173 T -> C LOC_Os03g39940.1 downstream_gene_variant ; 2722.0bp to feature; MODIFIER silent_mutation Average:14.149; most accessible tissue: Minghui63 panicle, score: 25.313 N N N N
vg0322195173 T -> DEL N N silent_mutation Average:14.149; most accessible tissue: Minghui63 panicle, score: 25.313 N N N N